Football Federation Australia may have another battle with an A-League club on its hands after the Newcastle Jets claimed they may have been overcharged to acquire their licence.

Hot on the heels of an attack from outspoken Gold Coast billionaire owner Clive Palmer over FFA's running of the game, the Jets on Tuesday released a statement claiming they were considering legal action over what they believed could be an excessive fee to take over the club.

Backing up comments made by Palmer on Tuesday night, the Jets - who were taken over by mining magnate Nathan Tinkler in late 2010 - said in a statement they were the "only owners to be charged a multi-million dollar fee" to take on a licence.

FFA on Tuesday night rejected any suggestions the Jets had been misled on licence fees.

"There is a difference between a licence fee and an acquisition fee and the distinction is important," A-League chief Lyall Gorman said.

"The acquisition fee for a licence is unique to each club and reflects the particular circumstances of that club and its market, its history, its success, its support, prior investment including by FFA, the potential of the market and other factors that are relevant to an assessment of value.

"In the case of the Jets, those market variables included the fact there was an established club with a successful history and strong supporter base in a traditional football area.

"The agreement by Hunter Sports Group to the acquisition price reflected those market factors and followed an open and comprehensive commercial negotiation and due diligence process."

Tinkler's Hunter Sports Group took over the ownership of the Jets in September, 2010 when FFA revoked former owner Con Constantine's licence.

The Jets' claims followed comments by Palmer on SBS's The World Game television show on Monday that: "We paid $500,000 for our licence. Poor old Nathan Tinkler had to fork out $7 million for his licence."

The Jets said in the statement they were charged a "substantial fee".

"This money was paid in good faith as the Jets were advised from the FFA it was a standard fee," it said.

"It has since become apparent at the time of acquisition; the Jets were the only owners to be charged a multi million-dollar fee.

"The Jets are currently reviewing this transaction and considering its legal options."

The Jets said they supported several other key points raised by Palmer, including clubs having greater input in the running of the A-League, increased transparency by the FFA and a change in the current commercial model of the A-League.

FFA commended Tinkler's impact on the club's supporters' base, membership and sponsorships since taking the helm.